This channel contains videos related to chemistry, such as tutorials for different chemical software. Despite the name, MacMolPlt is a cross-platform Chemistry visualization tool that can be used to build molecules with an integrated graphical. I also show how to identify the HOMO and LUMO canonical MOs in MacMolPlt. Note that I specify a geometry optimization in the GAMESS input. Despite the name, MacMolPlt is a cross-platform Chemistry visualization tool that can be used to build molecules with an integrated graphical. wxMacMolPlt: a visualizer for GAMESS-US. by IaNiusha. Play next; Play now. ORCA Quantum Chemistry Program, GNU/linux mint mate.
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One PI I am looking at has just gained their position, is there a similar question I could ask to this individual? Thanks for finding that, its pretty interesting!
However, I'm asking a bit more on the gritty how to do it side of things. Wxmacmolplt youtube I figure out how to use amber18, I could adapt procedures to literature, but so far I haven't been able to figure out how to set up and run a MD simulation. The problem I'm having is that I can't get an initial guess of the system to be in a form that the amber18 tools can read or vice versa? I have structure files of AOT, Isooctane, water. I've tried putting those into packmol to generate a rough RM, but then I need to apply antechamber to use gaff02 which isn't working you either generate an.
I've tried running antechamber on the structures by themselves and then using packmol, but the antechamber changes make wxmacmolplt youtube fiiles unreadable to packmol. I could theoretically build up the system in xLEaP, I guess, but that would involve adding a couple hundred molecules individually by hand, since I don't think theres an option to solvate with isooctane.
I've tried a few other approaches, but it's a bit tedious to list out and none have worked so far. Do you have any advice wxmacmolplt youtube that end of things?
First, see this tutorial uses packmol and wxmacmolplt youtube the gaff parameters needed to wxmacmolplt youtube the simulation. Taking the coordinates of a single example compound one at a time for each different component from your packmol generated system and therefore in packmol format and subjecting them to anterchamber and then parmchk individually after converting the packmol file type into a PDB format.
This should then wxmacmolplt youtube give you mol2 and. They should also be in the correct format that once at this point you can go to step 5 on the tutorial and load in your pdb and parameters.
If you're experiencing issues with the PDB files not being recognized then perhaps can you show the example coordinates that you are giving to antechamber. A common issue can be non-unique atom labelling for each compound. One thing I'm kind of unsure of with converting packmol. You just get a giant list of the thousand whatever atoms. Is that okay to use in amber? I was wxmacmolplt youtube little unclear on if there was some sort of VdW check to determine connectivity or not.
Also, if I use antechamber on individual molecules, how do I transfer the data generated there into the "master" wxmacmolplt youtube of all coordinates?
As far as I could tell, the biggest thing antechamber did wxmacmolplt youtube assign partial charges and assign atom types, which are in weird places of the file.
Definitely not okay. Each individual molecule should have its own "residue" number and then also each atom within that molecule should have a unique 4 characters or less identifier e. As shown in the first picture in the tutorial linked before you want each atom to be labelled with a unique identifier aka atom name wxmacmolplt youtube each molecule of it needs to be of a different residue number here, a fake 1 and 2 are shown e. Below is second occurrence of molecule with residue name XXX This line does not really exist in file.
Your overall PDB file needs to look something like this. Wxmacmolplt youtube you are getting out of packmol is an. Make wxmacmolplt youtube spit out a PDB instead as shown in the amber tutorial. I suspect the problem lies in your input PDBs you give packmol. These need to contain unique names for each atom, you should manually edit these input pdb files to make sure that is the case.
If you're still having trouble with this, show me the input Wxmacmolplt youtube file you are using I trust the geomtry etc. I suspect it will then spit out the overall PDB file back to you with those atom names saved to each molecule and each molecule numbered separately which you will want for amber. If you don't know the wxmacmolplt youtube site be sure to read up on approaches to blind docking can still be done with autodock. Sorry I should have given more info.
The two molecules I am separating are cellobiose. Wxmacmolplt youtube solvent is 1-butylmethylimidazolium acetate. I cannot change this now. Umbrella sampling would be instinctively the method of choice here to go for, especially as you want to be separating out over a certain distance range.
So can you explain in a little more detail how you set up the simulations and why you think its not giving good results? Weird looking FE profile e. My experience of umbrella sampling is it takes a few goes to get the collective variable wxmacmolplt youtube and restraints force s right but then your set.
Umbrella sampling is not perfect and like all free energy calculation methods, going to be somewhat noisy. If things really aren't working out then metadynamics or ABMD - arguably worse than metadynamics, but potentially easier to use if you use Amber as your md engine could be considered. But I would recommend trying umbrella unless it really isn't working out. I sell them and you can find them at porcupyne. The washing wxmacmolplt youtube is fixed too.
I replace shirts that have that problem asap. Its out of stock now: But still, no one has ever done this before? How do other people doing this calculate this?
Why aren't you doing the same? Other people use dimensional analysis to take into account the box size and density of water, which can both change. This is how my PI taught me, and how all of my collaborators calculate it. So, I am doing it the same. Again, not sure what you're getting at here.
It's not correct, you said it yourself movies in hd hollywood it's an approximation that will give you the wrong number as you increase the number of waters. What I depicted is correctwhat you depicted is wrong. Sometimes it can be useful, certainly, but without knowing the details of OP's system -- why introduce the possibility for error?
It's sloppy. Small things add wxmacmolplt youtube was the mantra of my undergraduate biochemistry course. Again, why introduce the possibility for error? It's just not good science. Why over-simplify things when they give wxmacmolplt youtube the wrong answer, which could read as: I don't see why you have such a hangup on using the correct form of the calculation.
I admit your form can be useful, but it is wrong, and saying it's correct is misleading. You should be aware that the method you propose too makes an approximation that the size of the water box does not change from initial build to equilbiration in the NPT ensemble. Go ask your PI and s he will tell you the same.
MD simulations are full of approximations, nothing wrong with both methods, go ask your PI, they will no doubt tell you the same. If ur in the us u can try coconut bliss wxmacmolplt youtube a rly good ice cream and its dairy free. Well with luck u can get it also outside the US. Have wxmacmolplt youtube got an enzyme wxmacmolplt youtube that has two catalytic centers, and they both perform stepwise roles?
An example enzyme for this is; wxmacmolplt youtube glycerol phosphate synthase, but I don't know if literature exists on what you want tbh. Wxmacmolplt youtube is rather rare wxmacmolplt youtube not unheard off in enzymes, and so if this is the case or you belive this to be auction market theory youtube er case you could look into literature on one of those types of enzymes.
Haha I was starting to think it was an unanswerable question so thank you for your response! I just added a little about how partial bonds occur and how the side chains are responsible for lowering the activation energy of the transition state, making it more stable.
Hey I too think you did give the write answer if this wxmacmolplt youtube a 2 mark questionyou just had a mean examiner. Perhaps they just wanted a little more elaboration. If you were to elaborate more, you could say how wxmacmolplt youtube enzymes primary role is bind the transition state which therefore stabilizes it and not the reactant 1so you can avoid the reorganisation penalty entropic that the substrate has to undergo associated with going from reactant to wxmacmolplt youtube state this is often fairly small, but in some substrates it can be quite significant.
The empirical part of semi-empirical methods means they have parameters fitted to reproduce experimental or very high level computational results. Therefore wxmacmolplt youtube can normally maybe say some are better than others for a certain class of molecules e.
You can look up in wxmacmolplt youtube literature papers where they compare these methods against different training sets aka different classes of molecules and see what seems best for your class wxmacmolplt youtube molecule. Also if your using gaussian, I would recommend considering PM6 or PM7 over the suggested functionals. Several factors can do into determining the 'best' wavelength, here are the things I would consider:. It is quite common practice to use the wavelength at the maximum wxmacmolplt youtube the peak as will get larger signal for same conc then at lower points along curve.
If it does, then chances are you wxmacmolplt youtube going to max out your detector from just the solvent, making measurement at this wavelength point impossible. Can't go below ish nm with methanol but with water you'd probably be fine at nm Google UV solvent cut off if want to find out more.
Perhaps there is a wavelength where one aosrbs and the other doesn't or at least doesn't significantly absorb? Regardless, a good background is needed to ensure you are just looking at your compound s of interests absorbance. Yes this was a huge help.
Just general curiosity lol but honestly that was a huge help. Thank you very much. The problem is avogadro is just connecting your atoms in the order you type them in. If you click on Display Settings There must be a way to add to that because you want more atoms connected than it comes up with naturally. Your 6 atom doesn't look like the picture above as far as I can tell, it looks like it's octahedral instead of see-saw.
Despite the name, MacMolPlt is a cross-platform Chemistry visualization tool that can be used to build molecules with an integrated graphical model builder, create input files for the GAMESS computational chemistry program, and then visualize the results of computational chemistry runs.
Features include a high-quality 3D display, animations of normal modes and reaction sequences and output wxmacmolplt youtube a variety of formats including high-quality images and QuickTime and Flash wxmacmolplt youtube. Version 7. Google Drive is more than an app or a website -- you can also install it on your PC. Turn your most meaningful text exchanges with a loved one into a memento that you'll cherish wxmacmolplt youtube Login or create an account to post a review.
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Full Specifications. Discover the latest Windows apps Be the first to know about the hottest apps with Download's Windows Apps newsletter. Several enhancements have been made to the display code. Options have been added to wxmacmolplt youtube 3D Pane of the prefernces for smooth shading with and without shadows. Added rudimentary support for Mopac files.
Improved support for Model Core Potentials. Improved the PDB file parser.